Variant report

Variant	rs62026661
Chromosome Location	chr15:45480316-45480317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr15:45480306-45480528	K562	blood:	n/a	n/a
2	TAF1	chr15:45479918-45480356	ECC-1	luminal epithelium:	n/a	n/a
3	TAF1	chr15:45479994-45480552	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr15:45480249-45480468	HepG2	liver:	n/a	n/a
5	SRF	chr15:45480221-45480330	GM12878	blood:	n/a	chr15:45480239-45480249
6	TAF1	chr15:45479913-45480457	HepG2	liver:	n/a	n/a
7	MAZ	chr15:45479981-45480473	HepG2	liver:	n/a	chr15:45480427-45480434 chr15:45480239-45480249 chr15:45480425-45480434
8	POLR2A	chr15:45480086-45481060	GM12892	blood:	n/a	n/a
9	ZNF263	chr15:45480253-45481019	HEK293-T-REx	kidney:	n/a	chr15:45480654-45480663 chr15:45480651-45480660 chr15:45480300-45480309 chr15:45480686-45480695
10	POLR2A	chr15:45480235-45481027	GM12892	blood:	n/a	n/a
11	TAF1	chr15:45480232-45480466	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr15:45480236-45480529	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr15:45480200-45480972	GM12891	blood:	n/a	n/a
14	POLR2A	chr15:45479977-45480806	IMR90	lung:	n/a	n/a
15	ZBTB7A	chr15:45480208-45480429	K562	blood:	n/a	n/a
16	POLR2A	chr15:45479982-45480606	SK-N-MC	brain:	n/a	n/a
17	TAF1	chr15:45479935-45480486	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr15:45480311-45480367	MCF-7	breast:	n/a	n/a
19	POLR2A	chr15:45479977-45480556	GM12878	blood:	n/a	n/a
20	TBP	chr15:45480094-45480500	H1-hESC	embryonic stem cell:	n/a	n/a
21	EGR1	chr15:45479617-45480332	GM12878	blood:	n/a	chr15:45480235-45480250 chr15:45480236-45480249 chr15:45479955-45479969 chr15:45480241-45480251 chr15:45480238-45480248 chr15:45480236-45480249 chr15:45480022-45480032 chr15:45480021-45480031
22	POLR2A	chr15:45479855-45481070	GM12878	blood:	n/a	n/a
23	POLR2A	chr15:45479893-45480443	K562	blood:	n/a	n/a
24	MAX	chr15:45480269-45480448	HepG2	liver:	n/a	chr15:45480427-45480434 chr15:45480425-45480434
25	POLR2A	chr15:45480046-45480418	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr15:45479923-45480478	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:45480220-45481151	GM12878	blood:	n/a	n/a
28	TEAD4	chr15:45480218-45480489	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr15:45480251-45480443	HepG2	liver:	n/a	n/a
30	REST	chr15:45480057-45480463	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr15:45480029-45480485	HepG2	liver:	n/a	n/a
32	POLR2A	chr15:45480273-45480409	A549	lung:	n/a	n/a
33	POLR2A	chr15:45480224-45480496	SK-N-SH	brain:	n/a	n/a
34	CHD2	chr15:45480088-45481036	GM12878	blood:	n/a	chr15:45480242-45480252 chr15:45480231-45480241
35	POLR2A	chr15:45480099-45480414	HepG2	liver:	n/a	n/a
36	RCOR1	chr15:45480287-45481040	GM12878	blood:	n/a	n/a
37	POU2F2	chr15:45480140-45481079	GM12878	blood:	n/a	chr15:45480233-45480245 chr15:45480238-45480250
38	POLR2A	chr15:45478871-45480608	HepG2	liver:	n/a	n/a
39	REST	chr15:45479956-45480883	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr15:45480020-45480452	SK-N-SH	brain:	n/a	n/a
41	MAZ	chr15:45479023-45481127	IMR90	lung:	n/a	chr15:45480427-45480434 chr15:45480239-45480249 chr15:45480425-45480434
42	POLR2A	chr15:45479943-45481057	H1-neurons	neurons:	n/a	n/a
43	TAF1	chr15:45479915-45480525	GM12878	blood:	n/a	n/a
44	POLR2A	chr15:45479947-45480508	HEK293	kidney:	n/a	n/a
45	MYC	chr15:45480314-45480489	MCF10A-Er-Src	breast:	n/a	chr15:45480427-45480434 chr15:45480425-45480434
46	YY1	chr15:45480230-45480532	GM12878	blood:	n/a	chr15:45480241-45480250
47	TAF1	chr15:45479941-45480876	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr15:45479952-45480918	GM15510	blood:	n/a	n/a
49	POU2F2	chr15:45480235-45480959	GM12891	blood:	n/a	chr15:45480238-45480250
50	POLR2A	chr15:45480246-45480924	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45465361..45468029-chr15:45478692..45480743,2	MCF-7	breast:
2	chr15:45457736..45460170-chr15:45478587..45480947,2	MCF-7	breast:
3	chr15:45457275..45460718-chr15:45477484..45481344,4	K562	blood:
4	chr15:45457610..45461525-chr15:45477333..45480560,5	MCF-7	breast:
5	chr15:45478077..45482452-chr15:45491020..45494377,5	MCF-7	breast:
6	chr15:45458222..45460718-chr15:45477355..45481212,4	K562	blood:
7	chr15:45465443..45468186-chr15:45479581..45482219,2	MCF-7	breast:
8	chr15:45477456..45480320-chr15:45491100..45493481,2	MCF-7	breast:
9	chr15:45471595..45473672-chr15:45478332..45480462,2	MCF-7	breast:

Variant related genes	Relation type
SHF	TF binding region
ENSG00000259932	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000138606	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10775129	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10851421	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10851422	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10851423	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11070444	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12323957	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12437603	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12438755	0.83[EUR][1000 genomes]
rs12440238	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12440321	0.80[AMR][1000 genomes]
rs12440793	0.81[ASN][1000 genomes]
rs12592055	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12593605	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12899786	0.86[EUR][1000 genomes]
rs12901114	0.80[AMR][1000 genomes]
rs12902212	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12904079	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12904331	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12905053	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12905246	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12906537	0.80[AMR][1000 genomes]
rs12906734	0.80[AMR][1000 genomes]
rs12908943	0.81[EUR][1000 genomes]
rs12909987	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12910270	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12913123	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12915027	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12915804	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12915965	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1648302	0.80[EUR][1000 genomes]
rs1648311	0.82[EUR][1000 genomes]
rs1706821	0.98[EUR][1000 genomes]
rs1706822	0.98[EUR][1000 genomes]
rs2292467	0.84[EUR][1000 genomes]
rs2467838	0.95[EUR][1000 genomes]
rs2899379	0.80[AMR][1000 genomes]
rs3959644	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4439707	0.80[AMR][1000 genomes]
rs60001836	0.81[EUR][1000 genomes]
rs62026665	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62026666	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167731	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7171401	0.80[AMR][1000 genomes]
rs7174913	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs753414	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040896	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
6	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	esv3339591	chr15:45478685-45481233	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
9	esv3450392	chr15:45479060-45481133	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45473200-45480400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:45477200-45480400	Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr15:45478200-45480600	Active TSS	Fetal Kidney	kidney
4	chr15:45478800-45480400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:45478800-45480400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:45479000-45480400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr15:45479000-45480600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr15:45479000-45481000	Active TSS	Ovary	ovary
9	chr15:45479000-45481200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr15:45479200-45480400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:45479200-45480400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr15:45479200-45480400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr15:45479200-45480400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:45479200-45480400	Active TSS	Psoas Muscle	Psoas
15	chr15:45479200-45480400	Bivalent/Poised TSS	GM12878-XiMat	blood
16	chr15:45479200-45480400	Active TSS	HUVEC	blood vessel
17	chr15:45479200-45480600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:45479200-45480600	Active TSS	Aorta	Aorta
19	chr15:45479200-45480600	Active TSS	Brain Substantia Nigra	brain
20	chr15:45479200-45480600	Active TSS	Fetal Lung	lung
21	chr15:45479200-45480600	Active TSS	Gastric	stomach
22	chr15:45479200-45480600	Active TSS	Placenta Amnion	Placenta Amnion
23	chr15:45479200-45480800	Active TSS	Brain Germinal Matrix	brain
24	chr15:45479200-45480800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:45479200-45481000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:45479200-45481000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr15:45479400-45480400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:45479400-45480400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:45479400-45480400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:45479400-45480400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr15:45479400-45480400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr15:45479400-45480400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
33	chr15:45479400-45480400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:45479400-45480400	Active TSS	Esophagus	oesophagus
35	chr15:45479400-45480400	Active TSS	Fetal Stomach	stomach
36	chr15:45479400-45480400	Active TSS	Pancreas	Pancrea
37	chr15:45479400-45480400	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr15:45479400-45480400	Active TSS	HSMMtube	muscle
39	chr15:45479400-45480400	Active TSS	Osteobl	bone
40	chr15:45479400-45480600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:45479400-45480600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:45479400-45480600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:45479400-45480600	Active TSS	Brain Anterior Caudate	brain
44	chr15:45479400-45480600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr15:45479400-45480600	Active TSS	Colon Smooth Muscle	Colon
46	chr15:45479400-45480600	Active TSS	Fetal Brain Male	brain
47	chr15:45479400-45480600	Active TSS	Left Ventricle	heart
48	chr15:45479400-45480600	Active TSS	Lung	lung
49	chr15:45479400-45480600	Active TSS	Rectal Smooth Muscle	rectum
50	chr15:45479400-45480600	Active TSS	HepG2	liver

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